Re: Accelerated MD with transmembrane protein

From: Felipe Merino (
Date: Fri Apr 11 2014 - 03:27:09 CDT


The rules for defining the acceleration parameters that you cite were
meant to be used with proteins primarily as far as i remember. Actually,
they are more a rule of thumb than anything else. For systems with
lipids the choice can a bit different as the dihedral energy per residue
on a lipid is quite different than an aminoacid.

Take a look at this paper, the define the parameters based directly on
the dihedral energy Miao Y, Nichols SE, McCammon JA (2014). Physical
Chemistry Chemical Physics 16(14):6398- 6406.

Have in mind that for big systems the acceleration (dV) gets a bit too
big and then in practice you cannot reweight the final distribution
simply because you average gets dominated by conformations that you
rarely sample (very high exp(dV*beta)

Being that said, I never saw my aMD simulations fail with a constraint
failure even with pretty huge acceleration (I even use it sometimes to
remove gross error from initial models) which
suggests that your systems have issues unrelated to the acceleration.

Hope that helps



On 04/10/2014 08:40 PM, Kevin Kastner wrote:
> Hello all! I am trying to use accelerated molecular dynamics on NAMD
> for a protein that is inside of a lipid bilayer and am having trouble.
> Previously, I had set up and run the simulation using the NAMD
> membrane tutorial and have gotten that to work (though I have
> converted it to use the amber force field instead of CHARMM). From
> other sources I have calculated the energies and alphas for each of
> the protein + system and the membrane to be the following:
> accelMDE = <dihedral energy from standard simulation> + 4 * (# of
> residues) + 40 * (# of POPC molecules)
> accelMDalpha = 1/5 * 4 * (# of residues) + 20 * (# of POPC molecules)
> accelMDTE = <total energy from standard simulation> - <dihedral energy
> from standard simulation> + 0.16 * (# of total atoms)
> accelMDTalpha = 0.16 * (# of total atoms)
> I have tried running with these new parameters both starting after
> the three preparation steps that need to be done with transmembrane
> systems (melting the lipid tails, then constraining the protein, and
> finally letting the whole system equilibrate) and also starting at the
> very beginning with the three steps using aMD, but the system crashes
> after a short while every time. Usually the error has to do with the
> SHAKE or RATTLE algorithms.
> Does anyone know anything else I need to do to get this to work? Do
> I need to reduce the size of the timesteps from 2fs to 1fs? Or do I
> need to do something else? Oh, I do not know if this makes a
> difference, but I am also trying to run this on GPUs, rather than
> CPUs. Is aMD not compatible with GPU-accelerated MD? I would
> appreciate any help that anyone can provide. Thank you!
> --
> - Kevin Kastner
> "For me, insanity is super sanity. The normal is psychotic. Normal
> means lack of imagination, lack of creativity." - Jean Dubuffet

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:42 CST